Job ID = 11632670 sra ファイルのダウンロード中... Completed: 912097K bytes transferred in 31 seconds (236589K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 48628515 spots for /home/okishinya/chipatlas/results/rn6/SRX3360108/SRR6253214.sra Written 48628515 spots for /home/okishinya/chipatlas/results/rn6/SRX3360108/SRR6253214.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:01 48628515 reads; of these: 48628515 (100.00%) were unpaired; of these: 31180619 (64.12%) aligned 0 times 14670286 (30.17%) aligned exactly 1 time 2777610 (5.71%) aligned >1 times 35.88% overall alignment rate Time searching: 00:14:05 Overall time: 00:14:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 10131122 / 17447896 = 0.5807 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 15 Feb 2019 05:44:01: # Command line: callpeak -t SRX3360108.bam -f BAM -g 2.15e9 -n SRX3360108.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3360108.10 # format = BAM # ChIP-seq file = ['SRX3360108.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 15 Feb 2019 05:44:01: #1 read tag files... INFO @ Fri, 15 Feb 2019 05:44:01: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 05:44:01: # Command line: callpeak -t SRX3360108.bam -f BAM -g 2.15e9 -n SRX3360108.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3360108.20 # format = BAM # ChIP-seq file = ['SRX3360108.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 15 Feb 2019 05:44:01: #1 read tag files... INFO @ Fri, 15 Feb 2019 05:44:01: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 05:44:01: # Command line: callpeak -t SRX3360108.bam -f BAM -g 2.15e9 -n SRX3360108.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3360108.05 # format = BAM # ChIP-seq file = ['SRX3360108.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 15 Feb 2019 05:44:01: #1 read tag files... INFO @ Fri, 15 Feb 2019 05:44:01: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 05:44:08: 1000000 INFO @ Fri, 15 Feb 2019 05:44:08: 1000000 INFO @ Fri, 15 Feb 2019 05:44:08: 1000000 INFO @ Fri, 15 Feb 2019 05:44:15: 2000000 INFO @ Fri, 15 Feb 2019 05:44:15: 2000000 INFO @ Fri, 15 Feb 2019 05:44:15: 2000000 INFO @ Fri, 15 Feb 2019 05:44:22: 3000000 INFO @ Fri, 15 Feb 2019 05:44:22: 3000000 INFO @ Fri, 15 Feb 2019 05:44:22: 3000000 INFO @ Fri, 15 Feb 2019 05:44:29: 4000000 INFO @ Fri, 15 Feb 2019 05:44:29: 4000000 INFO @ Fri, 15 Feb 2019 05:44:29: 4000000 INFO @ Fri, 15 Feb 2019 05:44:36: 5000000 INFO @ Fri, 15 Feb 2019 05:44:36: 5000000 INFO @ Fri, 15 Feb 2019 05:44:36: 5000000 INFO @ Fri, 15 Feb 2019 05:44:42: 6000000 INFO @ Fri, 15 Feb 2019 05:44:43: 6000000 INFO @ Fri, 15 Feb 2019 05:44:43: 6000000 INFO @ Fri, 15 Feb 2019 05:44:49: 7000000 INFO @ Fri, 15 Feb 2019 05:44:50: 7000000 INFO @ Fri, 15 Feb 2019 05:44:50: 7000000 INFO @ Fri, 15 Feb 2019 05:44:52: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 05:44:52: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 05:44:52: #1 total tags in treatment: 7316774 INFO @ Fri, 15 Feb 2019 05:44:52: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 05:44:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 05:44:52: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 05:44:52: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 05:44:52: #1 total tags in treatment: 7316774 INFO @ Fri, 15 Feb 2019 05:44:52: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 05:44:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 05:44:52: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 05:44:52: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 05:44:52: #1 total tags in treatment: 7316774 INFO @ Fri, 15 Feb 2019 05:44:52: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 05:44:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 05:44:52: #1 tags after filtering in treatment: 7316503 INFO @ Fri, 15 Feb 2019 05:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 05:44:52: #1 finished! INFO @ Fri, 15 Feb 2019 05:44:52: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 05:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 05:44:52: #1 tags after filtering in treatment: 7316503 INFO @ Fri, 15 Feb 2019 05:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 05:44:52: #1 finished! INFO @ Fri, 15 Feb 2019 05:44:52: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 05:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 05:44:52: #1 tags after filtering in treatment: 7316503 INFO @ Fri, 15 Feb 2019 05:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 05:44:52: #1 finished! INFO @ Fri, 15 Feb 2019 05:44:52: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 05:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 05:44:54: #2 number of paired peaks: 38589 INFO @ Fri, 15 Feb 2019 05:44:54: start model_add_line... INFO @ Fri, 15 Feb 2019 05:44:54: start X-correlation... INFO @ Fri, 15 Feb 2019 05:44:54: end of X-cor INFO @ Fri, 15 Feb 2019 05:44:54: #2 finished! INFO @ Fri, 15 Feb 2019 05:44:54: #2 predicted fragment length is 188 bps INFO @ Fri, 15 Feb 2019 05:44:54: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 15 Feb 2019 05:44:54: #2.2 Generate R script for model : SRX3360108.10_model.r INFO @ Fri, 15 Feb 2019 05:44:54: #3 Call peaks... INFO @ Fri, 15 Feb 2019 05:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 05:44:54: #2 number of paired peaks: 38589 INFO @ Fri, 15 Feb 2019 05:44:54: start model_add_line... INFO @ Fri, 15 Feb 2019 05:44:54: #2 number of paired peaks: 38589 INFO @ Fri, 15 Feb 2019 05:44:54: start model_add_line... INFO @ Fri, 15 Feb 2019 05:44:54: start X-correlation... INFO @ Fri, 15 Feb 2019 05:44:54: end of X-cor INFO @ Fri, 15 Feb 2019 05:44:54: #2 finished! INFO @ Fri, 15 Feb 2019 05:44:54: #2 predicted fragment length is 188 bps INFO @ Fri, 15 Feb 2019 05:44:54: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 15 Feb 2019 05:44:54: #2.2 Generate R script for model : SRX3360108.05_model.r INFO @ Fri, 15 Feb 2019 05:44:54: start X-correlation... INFO @ Fri, 15 Feb 2019 05:44:54: #3 Call peaks... INFO @ Fri, 15 Feb 2019 05:44:54: end of X-cor INFO @ Fri, 15 Feb 2019 05:44:54: #2 finished! INFO @ Fri, 15 Feb 2019 05:44:54: #2 predicted fragment length is 188 bps INFO @ Fri, 15 Feb 2019 05:44:54: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 15 Feb 2019 05:44:54: #2.2 Generate R script for model : SRX3360108.20_model.r INFO @ Fri, 15 Feb 2019 05:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 05:44:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 05:44:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 05:45:12: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 05:45:14: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 05:45:14: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 05:45:23: #4 Write output xls file... SRX3360108.20_peaks.xls INFO @ Fri, 15 Feb 2019 05:45:23: #4 Write peak in narrowPeak format file... SRX3360108.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 05:45:23: #4 Write summits bed file... SRX3360108.20_summits.bed INFO @ Fri, 15 Feb 2019 05:45:23: Done! pass1 - making usageList (72 chroms): 5 millis pass2 - checking and writing primary data (9940 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 05:45:26: #4 Write output xls file... SRX3360108.10_peaks.xls INFO @ Fri, 15 Feb 2019 05:45:26: #4 Write peak in narrowPeak format file... SRX3360108.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 05:45:26: #4 Write summits bed file... SRX3360108.10_summits.bed INFO @ Fri, 15 Feb 2019 05:45:26: #4 Write output xls file... SRX3360108.05_peaks.xls INFO @ Fri, 15 Feb 2019 05:45:26: Done! INFO @ Fri, 15 Feb 2019 05:45:26: #4 Write peak in narrowPeak format file... SRX3360108.05_peaks.narrowPeak pass1 - making usageList (109 chroms): 5 millis pass2 - checking and writing primary data (16905 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 05:45:26: #4 Write summits bed file... SRX3360108.05_summits.bed INFO @ Fri, 15 Feb 2019 05:45:27: Done! pass1 - making usageList (131 chroms): 6 millis pass2 - checking and writing primary data (21771 records, 4 fields): 34 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。